Question: Metadata sheet for DEXSeq analysis
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gravatar for A
19 months ago by
A40
A40 wrote:

Hi all, 

Just wondering if  anybody can offer some help. I have searched for this answer but unfortunately have not found any solutions

I am currently looking at an aging population of a specific cell type in various organs and am interested in looking for differential isoform usage over time. 

I have created a Granges object using the summarizedoverlap function for exon counting.and want to call the DEXSeq function. However, according to the vignette, I need to add the colData$ manually, but I have 95 samples, all of which contain different organs and 4 different time points (and soon these will be doubled, and further time points included).

Is there a way of assigning the sampledata sheet that I use for the DESeq pipeline to the summarized experiment output in order to call the Dexseq function to identify the samples and their respective time points, and then use ~time_point + Organ+ exon as the design?

Many thanks for all of your help!

ADD COMMENTlink written 19 months ago by A40
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